[Bioc-devel] RFC: xy2i and i2xy in *cdf packages

[Seth Falcon]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:
> I know the affy package doesn't use these functions, and a quick grep of 
> other packages that I thought might possibly use them came up empty as 
> well. Do you know of any packages that use these functions?
>
> Given the fact that they do get masked on loading of other cdf packages, 
> the apparent lack of use, and the existence of safer indices2xy() and 
> xy2indices() functions, I would advocate deprecation/deletion rather 
> than using a namespace.

Laurent, thanks for bringing this up (I know it is something you
mentioned in the past).  I like the idea of marking the functions in
the cdfpackages using .Deprecated() for this release.  In the next
cycle they can be .Defunct() and then gone.

I realize it likely overkill, but sticking to the deprecation cycle is
a good policy -- and if nobody is using them anyway, then the masking
isn't going to bite anyone :-)

Someone should send a note to the bioconducter list and announce that
these functions will be deprecated in the upcoming release (and
mention that there are alternatives in affy).

Best,

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org